Obviously I'm just gonna rewrite it, but I was annoyed this doesn't pass..... 
public class Solution {
    static String firstFilename;
    static String secondFilename;
    static String thirdFilename;
    static ArrayList<Integer> bytesFromFile = new ArrayList<>();
    static ArrayList<Integer> splitArrayOne = new ArrayList<>();
    static ArrayList<Integer> splitArrayTwo = new ArrayList<>();


    public static void main(String[] args) {
        ReadFilesAndInitialise();
        TransferBytesToArray();
        SplitTheArray();
        WriteBytesToFile(secondFilename, splitArrayOne);
        WriteBytesToFile(thirdFilename, splitArrayTwo);


    }

    public static void ReadFilesAndInitialise() {
        Scanner keyboardInput = new Scanner(System.in);
        firstFilename = keyboardInput.nextLine();
        secondFilename = keyboardInput.nextLine();
        thirdFilename = keyboardInput.nextLine();
        keyboardInput.close();
    }

    public static void TransferBytesToArray() {
        try {
            FileInputStream readFile = new FileInputStream(firstFilename);
            while (readFile.available() > 0) {
                bytesFromFile.add(readFile.read());
            }
            readFile.close();
        } catch (Exception e) {
            System.out.println("There was an exception reading the file");
        }
    }

    public static void SplitTheArray() {
        if (bytesFromFile.size() % 2 == 0) {
            int splitPoint = bytesFromFile.size() / 2;
            for (int i = 0; i < splitPoint; i++) {
                splitArrayOne.add(bytesFromFile.get(i));
            }
            for (int i = splitPoint; i < bytesFromFile.size(); i++) {
                splitArrayTwo.add(bytesFromFile.get(i));
            }
        } else {
            int splitPoint = (((bytesFromFile.size() - 1) / 2) + 1);
            for (int i = 0; i < splitPoint; i++) {
                splitArrayOne.add(bytesFromFile.get(i));

            }
            for (int i = splitPoint; i < bytesFromFile.size(); i++) {
                splitArrayTwo.add(bytesFromFile.get(i));

            }
        }
    }

    public static void WriteBytesToFile(String filename, ArrayList<Integer> splitArray) {
        try {
            FileOutputStream writeFile = new FileOutputStream(filename);

            for (Integer thisByte : splitArray) {
                writeFile.write(thisByte);
            }
            writeFile.close();
        } catch (Exception e) {
            System.out.println("There was an exception writing the files");
        }
    }


}